Source code is available on request. Please contact Oliver Homann at:
MochiView would not exist without the contributions of several excellent Java code libraries. Links to these libraries are provided below for any Java developers interested in utilizing them.
UCSC Genome Browser
website / paper / wiggle
While MochiView does not use any code from the UCSC Genome Browser, the design was heavily influenced by this archetypal genome browser. The design of some of MochiView’s database tables, including the binning strategy for storing locations (see ‘paper’ link above), was influenced by the browser. In addition, the design of the Tiled Set compressed data format was adapted from the description provided (see ‘wiggle’ link above) for the UCSC Browser’s wiggle file format.
The approach used for identifying genes enriched for a specific Gene Ontology term is adapted from the approach described for GO::TermFinder.
BioJava Cookbook / Thijs et al. paper
The Gibbs sampling code provided in the BioJava cookbook served as the template for the MochiView motif finder code (with substantial changes). The MochiView motif finder incorporates Markov model data into scoring alignments using the formula described by Thijs et al.
The statistical approach for identifying non-uniform positional distribution of motifs is adapted from the approach described by Casimiro et al.
website / paper
The support for Postion Specific Affinity Matrix (PSAM) motifs and the logo design for these motifs implements the concepts described for the motif-finding program MatrixREDUCE.
The calculation of Motif w-scores uses the technique described by Saurabh Sinha in the paper linked above.
The calculation of Motif p-values uses the technique described by Barash et al. in the paper linked above.
Fast Sequence Retrieval
The data transfer tool in MochiView does rapid sequence look-ups using a hash mapping technique described by Reneker and Shyu.
The code implementing modal windows in MochiView was adapted from code provided by Santhosh Kumar in his weblog.
Color blending was done using Jacob Dreyer’s LGPL ColorUtil class.
Fisher’s Exact Test
The code for this statistical test was written by Ed Buckler and can be found in the TASSEL bioinformatics package.
The algorithm behind the line smoothing option in MochiView’s plots was adapted from code posted by users “weihang” and “pstng” in a JFreeChart forum thread.
The MochiView executable relies upon certain free software libraries that are licensed under the terms of the GNU Library/Lesser General Public License (LGPL), Berkeley Software Distribution (BSD) license, Mozilla Public License v1.1, or Apache License v2.0, as the case may be. Acknowledgments, licensing terms and disclaimers for such libraries are contained in the documentation for each library, and your use of such material is governed by their respective terms. This third-party software is distributed here in the hope that it will be useful, but WITHOUT ANY WARRANTY, without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
MochiView License Overview
MochiView is available without fee, for academic, non-profit and commercial users. In order to prevent the sale of MochiView by third parties, the license (below) imposes restrictions on the redistribution of the software.
Copyright © 2007-2010 The Regents of the University of California.
All Rights Reserved.
Permission to use and copy this executable software and its documentation without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.
A separate written agreement signed by a duly authorized officer of The Regents of the University of California (“The Regents”) shall be required to (1) receive the source code, (2) to distribute the source code or derivative works, or (3) to incorporate this software into commercial products. Such permission may be obtained by contacting the University of California San Francisco through its Office of Technology Management, 185 Berry Street, Suite 4603, San Francisco, California 94107; http://otm.ucsf.edu.
This software program and documentation are copyrighted by The Regents. The software program and documentation are supplied “as is”, without any accompanying services from The Regents. The Regents does not warrant that the operation of the program will be uninterrupted or error-free. The end-user understands that the program was developed for research purposes and is advised not to rely exclusively on the program for any reason.
IN NO EVENT SHALL THE REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE AND ANY STATUTORY WARRANTY OF NON-INFRINGEMENT. THE SOFTWARE PROVIDED HEREUNDER IS ON AN “AS IS” BASIS, AND THE REGENTS HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.